Hi galaxy dev team:
I just installed galaxy on my ubuntu box and tried to do RNA-seq
analysis
according to Jeremy's excellent tutorial
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
however, I encountered following error messages when I was trying to
execute
Cufflinks in galaxy..
Dataset generation errors
Dataset 121: Cufflinks on data 92: gene expression
Tool execution generated the following error message:
Error running cufflinks. [Errno 2] No such file or directory:
'transcripts.gtf'
The tool produced the following additional output:
cufflinks v1.0.3
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4
-b
how should I solve this problem?
Thanks in advance.
Best Regards,
John Wu

John,
My best guess is that you are using bias correction but do not have
the needed reference genome(s) for the builds that you want to use.
See this page for instructions about setting up HTS tools; in
particular, you'll need to set up the sam_fa_indices.loc file:
https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
Best,
J.